Strictly anaerobic halophiles isolated from canned Swedish fermented herrings (Surströmming)

Fermented fish and fermented fish-based products, an ever-growing source of microbial diversity: A literature review

Fermented fish and fermented fish-based products are part of the diet of many countries all over the world. Their popularity is not only due to the unique flavor, the distinct texture, and the good nutritional quality, but also to the easiness of the production process, that is commonly based on empirical traditional methods. Fish fermentation techniques ususally rely on the combination of some key steps, including salting, addition of spices or additives, and maintenance of anaerobic conditions, thus selecting for the multiplication of some pro-technological microorganisms. The objective of the present review was to provide an overview of the current knowledge of the microbial communities occurring in fermented fish and fish-based products. Specific information was collected from scientific publications published from 2000 to 2022 with the aim of generating a comprehensive database. The production of fermented fish and fish-based foods was mostly localized in West African countries, Northern European countries, and Southeast Asian countries. Based on the available literature, the microbial composition of fermented fish and fish-based products was delineated by using viable counting combined with identification of isolates, and culture-independent techniques. The data obtained from viable counting highlighted the occurrence of microbial groups usually associated with food fermentation, namely lactic acid bacteria, staphylococci, Bacillus spp., and yeasts. The identification of isolates combined with culture-independent methods showed that the fermentative process of fish-based products was generally guided by lactobacilli (Lactiplantibacillus plantarum, Latilactobacillus sakei, and Latilactobacillus curvatus) or Tetragenococcus spp. depending on the salt concentration. Among lactic acid bacteria populations, Lactococcus spp., Pediococcus spp., Leuconostoc spp., Weissella spp., Enterococcus spp., Streptococcus spp., and Vagococcus spp. were frequently identified. Staphylococcus spp. and Bacillus spp. confirmed a great adaptation to fermented fish-based products. Other noteworthy bacterial taxa included Micrococcus spp., Pseudomonas spp., Psychrobacter spp., Halanaerobium spp., and Halomonas spp. Among human pathogenic bacteria, the occurrence of Clostridium spp. and Vibrio spp. was documented. As for yeast populations, the predominance of Candida spp., Debaryomyces spp., and Saccharomyces spp. was evidenced. The present literature review could serve as comprehensive database for the scientific community, and as a reference for the food industry in order to formulate tailored starter or adjunctive cultures for product improvement.

Factors affecting bacterial community dynamics and volatile metabolite profiles of Thai traditional salt fermented fish

Bacterial diversity of the Thai traditional salt fermented fish with roasted rice bran (Pla-ra) was investigated using classical and molecular approaches. Bacterial population of Pla-ra ranged from 10²-10⁶ in solid-state (SSF) and 10⁶-10⁹ CFU/g in submerged (SMF) fermentation types. Halanaerobium spp. and Lentibacillus spp. were the main genera particularly detected when rRNA analysis was applied. Tetragenococcus halophillus were dominant during the final stage in sea salt-recipe samples while Bacillus spp. were found in those rock salt recipes. In contrast, cultural plating demonstrated that Bacillus spp., generally B. amyloliquefaciens, were the dominant genera. In addition, B. pumilus, B. autrophaeus, B.subtilis and B. velezensis shown some relations with rock salt-recipe samples. The main volatile metabolites in all samples were butanoic acid and its derivatives. Key factors affected bacterial profiles and volatile compounds of salt fermented fish were type of salt, addition of roasted rice bran, and fermenting conditions.

Effects of Consuming Fermented Fish (Surströmming) on the Fecal Microflora in Healthy Individuals

Surströmming, a Swedish fermented fish, loved by some and avoided by others, occurs in many reports on improved or cured gastrointestinal problems even by a single meal. We tested the hypothesis that the microbes of the fermented food might have a potency to modify the gut microbiome. Two groups of voluntary participants (11 male, 8 female; aged 20-80 years) were exposed to a single meal containing the fish. A 7-day dietary intervention was carried out comprising the fish as the main source of protein in a single adult. The microbiome was characterized using 16S rRNA and metagenomic sequencing. Individual community-level changes in the microbiome were compared, as well as the presence of bacteria associated with the fermented fish. We focused on Shannon alpha and UniFrac beta diversity. We did not detect any global changes in the gut microbiome in response to Surströmming, nor were we able to recover and identify any members of Halanaerobium, which were associated with and abundant in the ingested fish, in the stool samples of the participants. Our results suggest that Surströmming consumption does not alter the microbiome of healthy individuals. However, beneficial effects on a diseased gut, impaired gut microbiome, or other effects in disease remain to be studied.

A Comprehensive Review with Future Insights on the Processing and Safety of Fermented Fish and the Associated Changes

As an easily spoiled source of valuable proteins and lipids, fish is preserved by fermentation in many cultures. Over time, diverse types of products have been produced from fish fermentation aside from whole fish, such as fermented fish paste and sauces. The consumption of fermented fish products has been shown to improve both physical and mental health due to the composition of the products. Fermented fish products can be dried prior to the fermentation process and include various additives to enhance the flavours and aid in fermentation. At the same time, the fermentation process and its conditions play a major role in determining the quality and safety of the product as the compositions change biochemically throughout fermentation. Additionally, the necessity of certain microorganisms and challenges in avoiding harmful microbes are reviewed to further optimise fermentation conditions in the future. Although several advanced technologies have emerged to produce better quality products and easier processes, the diversity of processes, ingredients, and products of fermented fish warrants further study, especially for the sake of the consumers' health and safety. In this review, the nutritional, microbial, and sensory characteristics of fermented fish are explored to better understand the health benefits along with the safety challenges introduced by fermented fish products. An exploratory approach of the published literature was conducted to achieve the purpose of this review using numerous books and online databases, including Google Scholar, Web of Science, Scopus, ScienceDirect, and PubMed Central, with the goal of obtaining, compiling, and reconstructing information on a variety of fundamental aspects of fish fermentation. This review explores significant information from all available library databases from 1950 to 2022. This review can assist food industries involved in fermented fish commercialization to efficiently ferment and produce better quality products by easing the fermentation process without risking the health and safety of consumers.

Genome-Resolved Metaproteomic Analysis of Microbiota and Metabolic Pathways Involved in Taste Formation During Chinese Traditional Fish Sauce (Yu-lu) Fermentation

Complex microbial metabolism is key to taste formation in high-quality fish sauce during fermentation. To guide quality supervision and targeted regulation, we analyzed the function of microbial flora during fermentation based on a previously developed metagenomic database. The abundance of most identified genes involved in metabolic functions showed an upward trend in abundance during fermentation. In total, 571 proteins extracted from fish sauce at different fermentation stages were identified. These proteins were mainly derived from Halanaerobium, Psychrobacter, Photobacterium, and Tetragenococcus. Functional annotation revealed 15 pathways related to amino acid metabolism, including alanine, aspartate, glutamate, and histidine metabolism; lysine degradation; and arginine biosynthesis. This study demonstrated the approaches to identify microbiota functions and metabolic pathways, thereby providing a theoretical basis for taste formation mechanisms during traditional fish sauce fermentation.

Prevalence of Histidine Decarboxylase Genes of Gram-Positive Bacteria in Surströmming as Revealed by qPCR

Histamine is a degradation product of the bacterial decarboxylation of the amino acid histidine; such activity is determined by histidine decarboxylase encoded by a gene cluster, carried by some Gram-positive bacteria, that includes the hdcA gene. In this study, the presence of the hdcA gene in ready-to-eat surströmming samples collected from three producers based in Sweden was directly assessed via qPCR analysis for the very first time. Samples from producer A showed hdcA average gene abundance of 6.67 ± 0.13 Log cells/gene copies g^-1; in samples from producer B the average value attested at 5.56 ± 0.06 Log cells/gene copies g^-1, whereas for samples of producer C hdcA average gene abundance attested at 5.30 ± 0.08 Log cells/gene copies g^-1. ANOVA showed a significantly higher average hdcA gene copy number in samples from producer A, whereas no significant differences were seen between average values of hdcA gene copy numbers detected in samples from producer B and C. The hdcA gene copies detected in the present study could give an estimation of the load of potential histamine-producing bacteria in surströmming.

Anti-Inflammatory Effects and Their Correlation with Microbial Community of Shindari, a Traditional Jeju Beverage

In this study, we investigated the microbial community and its correlation with anti-inflammatory effects during the fermentation procedure of shindari. Since shindari is traditionally manufactured through a fermentation process of 3–4 days in summer or 5–6 days in winter, the shindari materials applied in this study were fermented for 1, 3, and 5 days, respectively. Microbial community structure in the shindari manufacturing process was analyzed by Illumina MiSeq sequencing. Results revealed different fermentation time had different influences on the community structure and microbial diversity in the shindari process. Ultimately, we found that pathogenic bacteria such as Enterococcus durans (9.3%) and Enterobacter asburiae (4.5%) dominate the shindari fermented for 1 day, while samples with a fermentation period of more than 3 days occupied lactic acid bacteria such as Pediococcus sp. (97.1%). In addition, to study the relationship between fermentation period and anti-inflammatory effect in the shindari manufacturing process, we applied RAW264.7 cells, a classic cell model for inflammation studies. First, we prepared an ethyl acetate extract of shindari fermented for 1 (S1), 3 (S3), or 5 days (S5), and then it was confirmed that all of these extracts inhibited the nitric oxide (NO) production in a concentration-dependent manner. In addition, these inhibitory effects were correlated with the suppressive effect of shindari extracts against overexpression of inducible nitric oxide synthase (iNOS). Furthermore, S3 and S5 also inhibited the production of pro-inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and IL-6. Overall, the anti-inflammatory effect of S3 was suggested to be mediated through the negative regulation of mitogen-activated protein kinase signaling (MAPKs) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathways.

Dynamics of microbial communities, texture and flavor in Suan zuo yu during fermentation

Suan zuo yu is a traditional Chinese fermented product. We explored the microbial diversity, the dynamic changes of texture and flavor compounds at different fermentation times (up to 24 d). Results showed that Weissella and Lactobacillus may play a vital role in fermentation especially for the flavor. At the end of fermentation, the taste activity value of Asp, Glu, and His were 21.61, 17.29 and 7.73, respectively. The bound water increased gradually indicated by low-field nuclear magnetic resonance, and the hardness was also increased. During the whole fermentation process, the myosin heavy chain protein and actin decreased obviously. Gas chromatography-mass spectrometry showed that a total of 80 volatile compounds were detected, and 6 alcohols, 6 aldehydes and 6 esters increased significantly, which mainly contributed to the flavor of Suan zuo yu. This study provides a theoretical basis for the industrial production of fermented fish.

Discovering microbiota and volatile compounds of surströmming, the traditional Swedish sour herring

In this study, the microbiota of ready-to-eat surströmming from three Swedish producers were studied using a combined approach. The pH values of the samples ranged between 6.67 ± 0.01 and 6.98 ± 0.01, whereas their a_w values were between 0.911 ± 0.001 and 0.940 ± 0.001. The acetic acid concentration was between 0.289 ± 0.009 g/100 g and 0.556 ± 0.036 g/100 g. Very low concentrations of lactic acid were measured. Viable counting revealed the presence of mesophilic aerobes, mesophilic lactobacilli and lactococci as well as halophilic lactobacilli and lactococci, coagulase-negative staphylococci, halophilic aerobes and anaerobes. Negligible counts for Enterobacteriaceae, Pseudomonadaceae and total eumycetes were observed, whereas no sulfite-reducing anaerobes were detected. Listeria monocytogenes and Salmonella spp. were absent in all samples. Multiplex real-time PCR revealed the absence of the bont/A, bont/B, bont/E, bont/F, and 4gyrB (CP) genes, which encode botulinic toxins, in all the samples analyzed. Metagenomic sequencing revealed the presence of a core microbiota dominated by Halanaerobium praevalens, Alkalibacterium gilvum, Carnobacterium spp., Tetragenococcus halophilus, Clostridiisalibacter spp. and Porphyromonadaceae. Psychrobacter celer, Ruminococcaceae, Marinilactibacillus psychrotolerans, Streptococcus infantis and Salinivibrio costicola were detected as minor OTUs. GC-MS analysis of volatile components revealed the massive presence of trimethylamine and sulphur compounds. Moreover, 1,2,4-trithiolane, phenols, ketones, aldehydes, alcohols, esters and long chain aliphatic hydrocarbons were also detected. The data obtained allowed pro-technological bacteria, which are well-adapted to saline environments, to be discovered for the first time. Further analyses are needed to better clarify the extent of the contribution of either the microbiota or autolytic enzymes of the fish flesh in the aroma definition.

Exploring the Brine Microbiota of a Traditional Norwegian Fermented Fish Product (Rakfisk) from Six Different Producers during Two Consecutive Seasonal Productions

The purpose of this study was to explore the microbiota of Norwegian fermented fish (rakfisk), a traditional product popular in the Norwegian market. Brine samples, collected from six producers during two subsequent years, were used. The producers applied different salt concentrations (between 3.8% and 7.2% NaCl), ripening temperatures (between 3.5 and 7.5 °C), fish species (trout or char), and fish upbringing (wild trout, on-shore farmed trout or char, and off-shore farmed char). The microbiota in the brine during the ripening process was mainly characterized by DNA-based, culture-independent methods. In total, 1710 samples were processed and of these 1342 were used for the final analysis. The microbiota was dominated by Gammaproteobacteria and Bacilli with the largest variance between samples associated with the genera Psychrobacter and Lactobacillus. The variance in the material was mainly determined by the origin of the samples, i.e., the different producers. The microbiota from the individual producers was to a large extent reproducible from one year to the next and appeared to be determined by the relatively small differences in the salinity and the ripening temperature. This is the first study exploring the microbiota in rakfisk brine and it provides insights into environmental factors affecting the rakfisk ecosystems.

Quality, functionality, and microbiology of fermented fish: a review

Fermentation is a traditional food preservation method and is widely used for improving food safety, shelf life, and organoleptic and nutritional attributes. Fermented fish are produced and consumed in different parts of the world and are an integral part of many food cultures. Furthermore, fermented fish are a source of interesting microbes and are an important industry in many countries. This review tries to update the types and manufacturing processes for fermented fish around the world. The emphasis is on this work related to fermented fish and their health benefits, as well as the contribution of microorganisms to their fermentation. A variety of different approaches have been used to determine and understand microbial composition and functionality. Moreover, some challenges and future research directions regarding fermented fish are also discussed in this review. Further research into fermented fish products is of crucial importance not only for the food industry but also for human health. However, extensive in vivo and toxicological studies are essential before the application of bioactive-rich fermented fish products for human health benefits.

Review: Diversity of Microorganisms in Global Fermented Foods and Beverages

Culturalable and non-culturable microorganisms naturally ferment majority of global fermented foods and beverages. Traditional food fermentation represents an extremely valuable cultural heritage in most regions, and harbors a huge genetic potential of valuable but hitherto undiscovered strains. Holistic approaches for identification and complete profiling of both culturalable and non-culturable microorganisms in global fermented foods are of interest to food microbiologists. The application of culture-independent technique has thrown new light on the diversity of a number of hitherto unknown and non-cultural microorganisms in naturally fermented foods. Functional bacterial groups ("phylotypes") may be reflected by their mRNA expression in a particular substrate and not by mere DNA-level detection. An attempt has been made to review the microbiology of some fermented foods and alcoholic beverages of the world.

Ræstur fiskur: air-dried fermented fish the Faroese way

BACKGROUND

Fish has played an important role in the diet of the population of the mid-Atlantic Faroe Islands. Dried and fermented fish in particular have been an essential storable protein source in an economy where weather conditions and seasonal fluctuations affect the availability of food. For generations the islanders have prepared ræstur fiskur, a home-made air-dried and fermented fish dish made of Atlantic cod (Gadus morhua L.) or saithe (Pollachius virens (L.)). Fermenting the fish is an efficient and valuable cultural strategy for preserving fish.

METHODS

This ethnobiological study investigates the historical and present use of fermented fish in Faroese cuisine and examines its preservation as an everyday food that Faroese men pride themselves on making in high quality. This study is based on field notes collected through interviews and observations on the Faroe Islands since the mid-1990s.

RESULTS

Processed fish could be stored for a long period of time; this was important in an economy where weather conditions and seasonal fluctuations affect food availability dramatically. For this reason, home-made air-dried fish has been central to the food security of the Faroese people. Usually consumed with tallow from sheep, the dish was once appreciated customarily on Christmas Eve and New Year's Eve, but has been largely replaced by Danish dishes. However, it has survived as everyday food until today.

CONCLUSION

The presence of small-scale fishing, changing economic conditions, socially acquired taste-preferences, and the importance of old-fashioned dishes as key symbols of cultural identity, all contribute to the survival of ræstur fiskur in Faroese food culture. Today, the dish is not only an essential food source, but its consumption is also an important act of identification and solidarity with the national identity of the islanders.

Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State

Soap Lake is a meromictic, alkaline (∼pH 9.8) and saline (∼14–140 g liter^-1) lake located in the semiarid area of eastern Washington State. Of note is the length of time it has been meromictic (at least 2000 years) and the extremely high sulfide level (∼140 mM) in its monimolimnion. As expected, the microbial ecology of this lake is greatly influenced by these conditions. A bacterium, Halanaerobium hydrogeniformans, was isolated from the mixolimnion region of this lake. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium capable of forming hydrogen from 5- and 6-carbon sugars derived from hemicellulose and cellulose. Due to its ability to produce hydrogen under saline and alkaline conditions, in amounts that rival genetically modified organisms, its genome was sequenced. This sequence data provides an opportunity to explore the unique metabolic capabilities of this organism, including the mechanisms for tolerating the extreme conditions of both high salinity and alkalinity of its environment.

Analyzing the relation between the microbial diversity of DaQu and the turbidity spoilage of traditional Chinese vinegar

Vinegar is a traditional fermented condiment, and the microbial diversity of DaQu makes the quality of vinegar products. Recently, turbidity spoilage of vinegar sharply tampered with the quality of vinegar. In this study, the relation between the microbial diversity of DaQu and turbidity spoilage of vinegar was analyzed by plating technique, PCR-denaturing gradient gel electrophoresis (DGGE), and high-performance liquid chromatography (HPLC). The 16S rRNA sequencing and DGGE analysis indicated that Bacillus (Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus thuringiensis) and Lactobacillus (including Lactobacillus acidipiscis and Lactobacillus pobuzihii) species were the dominant contaminants in vinegar products. Meanwhile, DGGE analysis showed that the dominant bacteria in DaQu belonged to genera Bacillus, Lactobacillus, Pseudomonas, Weissella, Saccharopolyspora, Enterobacter, and Pantoea. However, only two yeast species (Pichia kudriavzevii and Saccharomycopsis fibuligera) and seven mold species including Aspergillus oryzae, Aspergillus niger, Aspergillus candidus, Rhizopus microspores, Eurotium herbariorum, Absidia corymbifera, and Eupenicillium javanicum were detected in the DaQu. The population level of fungi was below 5 log CFU/g in DaQu. The chemical and physical properties of vinegar and sediments were also determined. On the basis of a combined microbial diversity-chemical analysis, we demonstrated that turbidity spoilage of vinegar was a result of cooperation among the low population level and abundance of fungal species in DaQu, the suitable climate conditions, and the contaminants in vinegar. This is the first report to analyze the relation between the microbial diversity of DaQu and turbidity spoilage of vinegar.

Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL)

Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium, which in turn is the type genus of the family Halanaerobiaceae. The species is of interest because it is able to reduce a variety of nitro-substituted aromatic compounds at a high rate, and because of its ability to degrade organic pollutants. The strain is also of interest because it functions as a hydrolytic bacterium, fermenting complex organic matter and producing intermediary metabolites for other trophic groups such as sulfate-reducing and methanogenic bacteria. It is further reported as being involved in carbon removal in the Great Salt Lake, its source of isolation. This is the first completed genome sequence of a representative of the genus Halanaerobium and the second genome sequence from a type strain of the family Halanaerobiaceae. The 2,309,262 bp long genome with its 2,110 protein-coding and 70 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.